The formatting of the code/data and intent was hard for me to understand. But maybe this works for you?:

#!/usr/bin/perl -w
use strict;
use Data::Dumper;           # a core utility
use List::Util qw(shuffle); # a core utility

my @data;
while (<DATA>)
{
  next if /^\s*$/; #skip blank lines
  my ($important) = (split(' ',$_))[0];
  push @data, $important;
}

print Dumper \@data;  #debug - just to verify the split()

# so @data is about 100,000 entries
# this is a big array, but not that big

# the use of splice() works, but is relatively inefficient
# perhaps just use List::Util shuffle to randomize the
# indicies?

# This will create a list with 100,000 values
# but it will do it efficiently. 
# Within the parameters of what you have said,
# 1/4 million array/list elements will work ok, even on
# my wimpy Win XP32 bit machine

foreach my $index (shuffle (0..@data-1))
{
   print "$index $data[$index]\n";
}

=prints
VAR1 = [
          'FRZPY5Q02F00L9.ICM_AWP_Bv6.AWP_0001_2007_08_23',
          'FRZPY5Q02F00U8.ICM_AWP_Bv6.AWP_0001_2007_08_23',
          'FRZPY5Q02F01NC.ICM_AWP_Bv6.AWP_0001_2007_08_23',
          'FRZPY5Q02F023C.ICM_AWP_Bv6.AWP_0001_2007_08_23'
        ];
3 FRZPY5Q02F023C.ICM_AWP_Bv6.AWP_0001_2007_08_23
2 FRZPY5Q02F01NC.ICM_AWP_Bv6.AWP_0001_2007_08_23
1 FRZPY5Q02F00U8.ICM_AWP_Bv6.AWP_0001_2007_08_23
0 FRZPY5Q02F00L9.ICM_AWP_Bv6.AWP_0001_2007_08_23
=cut

__DATA__
FRZPY5Q02F00L9.ICM_AWP_Bv6.AWP_0001_2007_08_23 ACTGCCAACGCGCAGAACCTTAC
+CAGGTCCTGACTTCCTGACTATGGTTATTAGAAATAA TTTCCTTCAGTTCGGCTGGGTCAGTGACAGG
+TGATGCATGGCCGTC
FRZPY5Q02F00U8.ICM_AWP_Bv6.AWP_0001_2007_08_23 ACTGCCTAACCGATGAACCTTAC
+CTACACTTGACATGCAGAGAACTTTCCAGAGATGGAT TGGTGCCTTCGGGAACTCTGACACAGGTGAT
+GCATCGCCGTC 
FRZPY5Q02F01NC.ICM_AWP_Bv6.AWP_0001_2007_08_23 ACTGCCTACGCGAAGAACCTTAC
+CTACACTTGACATACAGAGAACTTACCAGAGATGGTT TGGTGCCTTCGGGAACTCTGATACAGGTGAT
+GCATGGCTGTC
FRZPY5Q02F023C.ICM_AWP_Bv6.AWP_0001_2007_08_23 ACTGCCAACGCGCAGAACCTTAC
+CAACCCTTGACATCCAGAGAATTTTCTAGAGATAGAT TTGTGCCTTCGGGAACTCTGTGACAGGTGAT
+GCATGGCTGTC
[download]

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